Biology subjects

Anderson, S. C.

Publications and source records attributed to Anderson, S. C..

13 recordsLinked to original sources

bioRxiv2026

Thermal niche warming is more consistent than range shifts in marine species under climate change

Marine species are widely expected to shift poleward or into deeper waters in response to rising ocean temperatures. However, our knowledge is primarily based on studies examining range shifts along single dimensions at a time (e.g., latitude or depth). Failing to address how movements along multiple dimensions interact, including associated changes in thermal exposure, may result in misleading conclusions and predictions of species distribution and community composition under global warming. To address this knowledge gap, we here develop and apply a multidimensional framework that jointly evaluates climate-driven redistribution of marine fish across latitude, longitude, depth and realized thermal niches, based on long-term scientific bottom-trawl surveys throughout the North Atlantic and Northeast Pacific. Our results show that net redistributions are generally small and highly region-specific, while the realized thermal niches of species have warmed substantially over the past three decades. These findings demonstrate that spatial redistribution is generally failing to keep pace with rising temperatures and challenge the prevailing assumption that marine species will move to escape warming. This has direct implications for biodiversity indicators that rely on distributional shifts as evidence of climate impacts, as well as climate-informed management and conservation of marine ecosystems, fisheries, and biodiversity at large.

ecology↗

bioRxiv2025

Groundfish with diverse life histories increase in size and abundance with proximity to spatial protections

Detecting positive responses to marine spatial protections, both in situ and as spillover effects, is critical for fisheries management yet difficult in practice. We leveraged 18 years of data on 28 groundfish species collected by four Indigenous Nations in Pacific Canada to assess ecological responses to spatially protected Rockfish Conservation Areas (RCAs). Body sizes and abundances were greatest inside RCAs and increased with proximity to RCAs at unprotected sites up to 160 km away. Abundance responses emerged faster (at younger RCA ages) for species with high rmax, as predicted, but body size responses emerged faster for species with low rmax, counter to predictions. Our study illustrates a general framework for jointly inferring in situ recovery and spillover benefits using a novel hierarchical geostatistical model that integrated long time series; observations made inside, near, and far from seven RCAs; and multiple species and survey methods spanning a 500-m depth range.

ecology↗

bioRxiv2025

Approximating spatial processes with too many knots degrades the quality of probabilistic predictions

Spatial and spatiotemporal models are increasingly critical for understanding species distributions, tracking population change, and informing conservation decisions. As biological processes are influenced by increasing external pressures, including human disturbance or environmental change, accurate model predictions become essential for adaptive management. However, the reliability of spatial predictions depends on often-overlooked modelling choices, including the spatial resolution used to approximate underlying processes. Using long term monitoring data from a large-scale groundfish survey in the California Current ecosystem, we investigated how spatial model complexity affects the quality of ecological predictions and derived indices used for management. We fit spatial and spatiotemporal models of ocean temperature and fish biomass density for 27 commercially important species using varying levels of spatial resolution. We evaluated both in-sample and out-of-sample prediction, and effects on area-weighted biomass indices. Counter to common assumptions, increasing spatial approximation resolution did not universally improve predictions. Our case studies demonstrate that for many datasets, out-of-sample prediction quality peaked at intermediate spatial resolutions and declined at the finest scales. Through simulation testing, we found this pattern was strongest when spatial patterning had a small range and high spatial variance, and observation error was low. For most species, spatial resolution had a minimal effect on biomass trend estimates used in management, but for several commercially important rockfish species, resolution choices substantially affected both the scale and uncertainty of population indices. Our findings demonstrate that spatial model specification can substantially affect ecological inference, with direct implications for management and conservation planning. We provide practical guidance for ecologists on selecting appropriate spatial complexity through cross-validation. When out-of-sample prediction is a focus, appropriate approximation complexity should improve both parameter estimation accuracy and derived quantities.

ecology↗

bioRxiv2025

Changes in body size with age do not follow the temperature-size rule

The temperature size-rule is often described as a reduction in ectothermic body size with warming. This coincides with the expectation that faster growth under warming would lead to larger sizes early in life but smaller sizes later in life. Here, we use > 99,000 observations of weight-at-age of four commercially-important fishes over 25 years to ask whether changes in size and growth can be explained by temperature. We also examine whether oxygen, a key part of a proposed mechanism behind the temperature size-rule, explains patterns of weight-at-age better than temperature. Changes in weight-at-age over time were more related to temperature than oxygen but the effect of temperature on weight was small and did not vary by age, counter to the temperature size-rule. Importantly, these results were sensitive to how the relationship between weight-at-age and temperature was modeled. While the functional form (linear or polynomial) mattered little, how space was included in the model led to different conclusions regarding how temperature affects size and growth. Assuming that spatial and spatiotemporal random effects - those that account for the higher degree of similarity between observations collected closer in space and time - are shared across ages led to different results compared to allowing these effects to vary by age. Models with shared effects suggested weight for younger ages had positive relationships with temperature and negative relationships for older ages. However, these models provided spurious support for the temperature size-rule as they had less statistical support than models that allowed spatial effects to vary by age. Overall, our work highlights that relationships among size, growth, temperature, and oxygen may not be as straightforward as theory suggests and illustrates that modeling decisions can have a large effect on tests of ecological theory, and more broadly, our ability to understand biological responses to climate change.

ecology↗

bioRxiv2025

Prevalence of the parasitic copepod, Sarcotaces sp., infection in British Columbia rockfishes (Sebastes sp.) and implications for rockfish life-history

Marine fishes often suffer detrimental effects of parasitism, which can affect multiple life-history traits, such as maturity, growth, fecundity, and mortality. Rockfishes (genus Sebastes), in the northeast Pacific Ocean, are commonly parasitized by copepods in the genus Sarcotaces. These copepods form large cysts within the body cavity, or in the musculature of individuals. There is a lack of baseline data on the prevalence of Sarcotaces sp. infection and the effect of infection on rockfish health and life-history. Here, we present data on Sarcotaces sp. infection in 23 rockfish species (including two thornyhead species, genus Sebastolobus) that includes over 37,000 individual records collected on Fisheries and Oceans Canadas (Pacific Region) groundfish research surveys. Sarcotaces sp. were found in all geographic areas covered by the surveys (the coastal waters of British Columbia), and at all depths fish were encountered. Infection rates in the various species ranged from 0% to 10%, and were highest for Pacific Ocean Perch (POP), Silvergray, Rougheye/Blackspotted Complex (REBS), Yellowmouth, and Yelloweye rockfishes. We found that Sarcotaces sp. infection shifted the length-at-maturity ogive, with infected individuals maturing at larger sizes--particularly for males, who exhibited a 22.3 mm increase (95% CrI [credible interval]: 5.5, 39.8) in length-at-maturity across species. For most species, this effect was greater in males than in females, and the effect was most pronounced in POP, Silvergray, and REBS rockfish. Moreover, we found that immature males were 2.5 times more likely to be infected than mature males (95% CrI: 1.3, 4.7) and immature females were 1.7 times more likely to be infected than mature females (95% CrI: 0.9, 3.0). While speculative, this is consistent with Sarcotaces sp. infection acting as a co-morbidity, possibly affecting fish health and the probability of perishing before reaching maturity. Body condition was largely unrelated to infection status; however, a slight increase ({approx} 5%) in condition was associated with infection in REBS, Yelloweye, and Yellowmouth rockfishes. To our knowledge, this is the first large-scale report on Sarcotaces sp. infection within rockfishes and on rockfish life-history traits. Future work is needed to elucidate how infection influences other life-history traits and, importantly, whether these changes affect key stock assessment parameters and, ultimately, catch advice provided to fisheries managers.

ecology↗

bioRxiv2025

Weak effects of local prey density and spatial overlap on predation intensity in a temperate marine ecosystem

Quantifying the impact of lower trophic level species abundance on higher trophic level predators (and vice versa) is critical for understanding marine ecosystem dynamics and for implementing ecosystem-based management. Trophic ecosystem models generally predict a tight coupling between prey and fish predators, such that higher abundance of lower trophic species increases abundance of higher trophic level predators. This assumes that predator feeding rates are limited by prey availability to some degree. Despite being a key component of predator-prey interactions and multi-species fisheries management, relatively few studies have assessed the impacts of prey availability on predation patterns of mobile, generalist fish predators using spatiotemporal models and local-scale stomach content, predator, and prey data. In this study, we explore the association between local density of key prey and predator stomach contents, and predator-prey spatiotemporal overlap and predation indices, using the Baltic Sea as a case study. We use three decades of spatially resolved biomass and stomach content data on Atlantic cod (Gadus morhua), and biomass data on three of its key prey: herring (Clupea harengus), the isopod Saduria entomon, and sprat (Sprattus sprattus). Using geostatistical generalized linear mixed effects models fitted to relative biomass density and prey-weight-per-predator-weight, we estimate spatiotemporal trends and annual indices of biomass weighted and area-expanded per-capita and population-level predation, predator-prey overlap, and the correlation between these indices. Range shifts have resulted in reduced predator-prey overlap over time, which is now the lowest in three decades. For Saduria, we find an association between prey availability and stomach contents, but not for herring or sprat. Similarly, only in Saduria do we find a positive correlation between population-level predation indices and the spatiotemporal overlap. Although behavioral interactions with pelagic prey are challenging to infer from stomach content and acoustic data due to high mobility leading to fine-scale spatiotemporal mismatch, the weak connection with local-scale availability, and low correlation between population-level predation and spatial overlap, could imply weaker coupling between pelagic prey and cod than previously thought. These findings provide key information on the strength of species interactions, which is crucial for the continued development of multispecies models and ecosystem-based fisheries management.

ecology↗

bioRxiv2025

'surveyjoin': A Standardized Database of Fisheries Bottom Trawl Surveys in the Northeast Pacific Ocean

Fisheries management faces challenges due to political, spatial, and ecological complexities, which are further exacerbated by variation or shifts in species distributions. Effective management depends on the ability to integrate fisheries data across political and geographic boundaries. However, such efforts may be hindered by inconsistent data formats, limited data sharing, methodological differences in sampling, and regional governance differences. To address these issues, we introduce the surveyjoin R package, which combines and provides public access to bottom trawl survey data collected by NOAA Fisheries and Fisheries and Oceans Canada in the Northeast Pacific Ocean. This initial database integrates over 3.3 million observations from 14 bottom trawl surveys spanning Alaska, British Columbia, Washington, Oregon, and California from the 1980s to present. This effort standardizes variables such as catch-per-unit-effort (CPUE), haul data, and in-situ measurements of bottom temperature. We demonstrate the utility of this database through three case studies. Our first case study develops a coastwide biomass index for Pacific hake (Merluccius productus) using geostatistical index standardization, comparing results to independent acoustic survey estimates. The second case study examines changes in the spatial distribution of groundfish species across marine heatwave and non-heatwave years, highlighting species-specific and community-level responses to warming events. Our third example applies spatially varying coefficient models to assess sablefish (Anoplopoma fimbria) biomass trends, identifying regional variability in increases in occurrence and biomass. Together, these case studies demonstrate how the surveyjoin R package and database may improve species and ecosystem assessments by providing insights into population trends across geopolitical boundaries. This database and package represent an important step toward offering a scalable framework that can be extended to include additional data types, surveys, and species. By fostering collaboration, transparency, and data-driven decision-making, surveyjoin supports international efforts to sustainably manage shared marine resources under dynamic environmental conditions.

ecology↗

bioRxiv2024

Estimating scale-dependent covariate responses using two-dimensional diffusion derived from the SPDE method

O_LISpecies distribution models (SDMs) are widely used to standardize spatially unbalanced data, project climate impacts, and identify habitat for conservation. SDMs typically estimate the impact of local environmental conditions by estimating a dome-shaped or non-parametric "environmental response function". However, ecological responses often integrate across local habitat conditions, such that species density depends on habitat at the location of sampling but also at nearby locations. C_LIO_LITo address this, we extend methods from the Stochastic Partial Differential Equation (SPDE) method that is widely used in INLA, which approximates spatial correlations based on local diffusion over a finite-element mesh (FEM). We specifically introduce the sparse inverse-diffusion operator on a FEM, and apply this operator to covariates to efficiently calculate a spatially weighted average of local habitat that is then passed through pointwise basis-expansion to predict species densities. We show that this operator has several useful properties, i.e., conservation of mass, linear computational time with spatial resolution, and invariance to linear (scale and offset) transformations of covariates. C_LIO_LIWe test this covariate-diffusion method using a simulation experiment, and show that it can correctly recover a non-local environmental response while collapsing to a local (pointwise) response when warranted. We apply it to monitoring data for 25 bottom-associated fishes in the eastern Bering Sea and 20 bird species in the western United States. This application confirms that non-local responses in the eastern Bering Sea case study are parsimonious for 26 species-maturity combinations, while 18 collapse to the pointwise method. Estimates suggest that some species-maturity combinations avoid proximity to the continental slope, beyond what is predicted by local bathymetry in isolation. By contrast, in four of the 20 bird species is the diffused human population density covariate more parsimonious than the original covariate. C_LIO_LIThe covariate-diffusion method introduced here constitutes a fast and efficient approach to modelling non-local covariate effects. This flexible method may be useful in cases when covariates influence nearby population densities, for instance due to movement of the sampled species or its important biological or physical drivers. C_LI

ecology↗

bioRxiv2024

Quantifying competition between two demersal fish species from spatiotemporal stomach content data

Inference on competition is often made on indirect patterns of potential competition, such as population trends and spatiotemporal overlap in diet and distribution. However, these indicators do not test if the contested resources are limited in supply, nor if they decline as competitor biomass increases. Using stomach content and biomass data, we evaluate food competition between Atlantic cod (Gadus morhua) and flounder (Platichthys spp.) in the Baltic Sea. We quantify diet overlap and fit geostatistical mixed models to evaluate effects of local-scale covariates on stomach contents. The dietary overlap is low and does not decline with predator density. We find that cod feed less on the isopod Saduria entomon at high flounder densities. However, the total prey weight in cod is not affected by flounder densities. This suggests interspecific food competition is not limiting the overall feeding of cod, but affects its diet composition. In addition, we find support for intraspecific food competition in large cod and flounder. Our study illustrates the importance of local-scale processes when inferring competition from stomach content data.

ecology↗

bioRxiv2022

Evaluating drivers of spatiotemporal individual condition of a bottom-associated marine fish

An organisms body condition describes its mass given its length and is often positively associated with fitness. The condition of Atlantic cod (Gadus morhua) in the Baltic Sea has declined dramatically since the early 1990s, possibly due to increased competition, food limitation, and hypoxia. However, the effect of biotic and abiotic variables on body condition have not been evaluated at local scales, which is important given spatial heterogeneity. We evaluate changes in distribution, experienced environmental conditions, and individual-level condition of cod in relation to covariates at different spatial scales using geostatistical models with spatial and spatiotemporal random effects. Oxygen, sprat biomass, and temperature were positively related to condition, and depth negatively associated, but the effect sizes of these variables were small--spatial and spatiotemporal latent variables explained almost five times more variation than fixed effects. We also show that accounting for the heterogenous distribution of cod leads to both lover levels and steeper trends over time in experienced oxygen compared to those in the environment. Understanding the drivers of spatiotemporal variation in body condition is critical for predicting responses to environmental change and to effective fishery management; yet low explanatory power of covariates on individual condition constitutes a major challenge.

ecology↗

bioRxiv2022

sdmTMB: an R package for fast, flexible, and user-friendly generalized linear mixed effects models with spatial and spatiotemporal random fields

Geostatistical spatial or spatiotemporal data are common across scientific fields. However, appropriate models to analyse these data, such as generalised linear mixed effects models (GLMMs) with Gaussian Markov random fields (GMRFs), are computationally intensive and challenging for many users to implement. Here, we introduce the R package sdmTMB, which extends the flexible interface familiar to users of lme4, glmmTMB, and mgcv to include spatial and spatiotemporal latent GMRFs using an SPDE-(stochastic partial differential equation) based approach. SPDE matrices are constructed with fmesher and estimation is conducted via maximum marginal likelihood with TMB or via Bayesian inference with tmbstan and rstan. We describe the model and explore case studies that illustrate sdmTMBs flexibility in implementing penalised smoothers, non-stationary processes (time-varying and spatially varying coefficients), hurdle models, cross-validation and anisotropy (directionally dependent spatial correlation). Finally, we compare the functionality, speed, and interfaces of related software, demonstrating that sdmTMB can be an order of magnitude faster than R-INLA. We hope sdmTMB will help open this useful class of models to a wider field of geostatistical analysts.

ecology↗

bioRxiv2021

Trends in Pacific Canadian groundfish stock status

We assembled estimated biomass (B) time series from stock assessments for 24 Pacific Canadian groundfish stocks and modelled average and stock status through 2020 based on biomass relative to each stocks (1) Limit Reference Point (B/LRP), (2) Upper Stock Reference (B/USR), and (3) biomass at maximum sustainable yield (B/BMSY). The overall mean B/LRP in 2020 was 3.2 (95% credible interval [CI]: 2.6-3.9). The overall mean B/USR and B/BMSY in 2020 was 1.5 (95% CI: 1.3-1.9) and 1.4 (95% CI: 1.1-1.7), respectively. Average stock status declined from 1950 to around 2000 and has remained relatively stable since then. The change around 2000 followed the implementation of ITQs (individual transferable quotas) for the trawl fleet and the commencement of the synoptic trawl surveys. As of their last assessment, four stocks (Strait of Georgia Lingcod [Area 4B], coastwide Bocaccio, and inside and outside Quillback Rockfish) had a greater than 5% probability of being below their LRP (i.e., in the " critical zone"); Pacific Cod in Area 3CD had a 4.6% probability. Roughly one-third of stocks had a greater than 1 in 4 chance of being below their USR (i.e., in the " cautious zone"). Conversely, two-thirds of assessed groundfish stocks had a high (>75%) probability of being above the USR (i.e., in the " healthy zone").

ecology↗

bioRxiv2020

Are we ready to track climate-driven shifts in marine species across international boundaries? - A global survey of scientific bottom trawl data

Marine biota is redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of data availability, and mismatch between data and real species distributions. To assess the extent of this challenge, we review the global status and accessibility of ongoing scientific bottom trawl surveys. In total, we gathered metadata for 283,925 samples from 95 surveys conducted regularly from 2001 to 2019. 59% of the metadata collected are not publicly available, highlighting that the availability of data is the most important challenge to assess species redistributions under global climate change. We further found that single surveys do not cover the full range of the main commercial demersal fish species and that an average of 18 surveys is needed to cover at least 50% of species ranges, demonstrating the importance of combining multiple surveys to evaluate species range shifts. We assess the potential for combining surveys to track transboundary species redistributions and show that differences in sampling schemes and inconsistency in sampling can be overcome with vector autoregressive spatio-temporal modeling to follow species density redistributions. In light of our global assessment, we establish a framework for improving the management and conservation of transboundary and migrating marine demersal species. We provide directions to improve data availability and encourage countries to share survey data, to assess species vulnerabilities, and to support management adaptation in a time of climate-driven ocean changes.

ecology↗